Returning to Europe with Napoleon, he was present at Marengo (1800) as second-in-command of the Consular Guard. General Jean Lannes, commanding a corps at Marengo, felt he didn't support his faltering troops sufficiently and a long running feud arose between them. At the close of the battle, Bessières led a successful cavalry charge with the Guard Cavalry though its effect on the battle was not as decisive as Napoleon pretended.[1] It was General François Étienne de Kellermann´s cavalry charge that won the battle for Marengo but Napoleon gave the credit largely to his own Guard Cavalry.

Promoted to general of division in 1802, he was subsequently promoted to Marshal of France in 1804, a wholly undeserved distinction based on his loyalty and friendship with Napoleon.[1]Auguste de Marmont, a future Marshal, said that if Bessières can be made a Marshal, then everyone can be one. He was also made colonel-general of the Guard Cavalry and would command them in all future campaigns where he proved a very able cavalry commander.

In 1805 he received the Grand Eagle of the Legion of Honour, and in 1809 was entitled Duke of Istria, or duc d'Istrie. It was a duché grand-fief, a rare, nominal, but hereditary honor (extinguished in 1856) in Napoleon's own Kingdom of Italy.[1]

With the outbreak of the Peninsular War, Marshal Bessières had his first opportunity of an independent command. He did well against the Spaniards, scoring a crushing victory in the Battle of Medina del Río Seco (1808),[1] but proved slow and hesitant in command of a large all-arms forces. Bessières was thus soon recalled to lead the Guard Cavalry during Napoleon´s invasion of Spain, a task more befitting his talents.

As war erupted in 1809 against Austria, he was again with the Grande Armée in the Danube valley as a cavalry leader, a position in which he excelled. At Essling, he led the cavalry in the centre and did a fine job holding it against superior numbers,[1] but once again fell foul of Marshal Lannes. Lannes again felt that Bessières was not providing sufficient support to his faltering troops and ordered him to charge home instead of malingering. Bessières then challenged Lannes to a duel. Marshal André Massena intervened and prevented the duel between two marshals in front of their troops.

At the subsequent Battle of Wagram, Bessières once again led the cavalry reserve and had a horse killed under him which caused consternation amongst the Guard.[1] Napoleon congratulated him on making his Guard cry but also chided him for not netting more prisoners because he lost his horse.

Replacing Jean-Baptiste Bernadotte in the command of the Army of the North a little later in the same year, the newly created Duke of Istria successfully opposed the British Walcheren expedition. In 1811, he was sent back to Spain again to lead the Army of the North.[1] He mostly fought counter-insurgency operations and proved a difficult and touchy colleague to his fellow army commanders, especially Marshal Masséna who was in dire need of support after his failed invasion of Portugal in 1810-1811. He was recalled in some disgrace and once again reverted to his habitual Guard Cavalry post.

For the Russian campaign in 1812, he commanded the enlarged Guard Cavalry. Hardly engaged at the Battle of Borodino, he destroyed his reputation with the rest of the army when he advised Napoleon not to use his Guard for a decisive breakthrough. Although this left the Imperial Guard intact for future battles, it prevented a decisive victory which might have successfully ended the Russian campaign.

With Joachim Murat back in Naples at the beginning of the 1813 campaign, Bessières was appointed to the command of the whole of Napoleon's cavalry.

Three days after the opening of the campaign, while reconnoitering the defile of Poserna-Rippach, Bessières was killed by a cannonball which ricocheted off a wall and hit him in the chest. [1] He died instantly. Napoleon deeply felt the loss of one of his truest friends while the remaining Marshals considered it a good death for a soldier.

After his death, Bessières was found to be heavily in debt after spending his fortune on his mistress. Napoleon oversaw his inheritance, settled most of his debts, and looked out for the future of his children. His eldest son was made a member of the Chamber of Peers by Louis XVIII.[1]

As a commander, Bessières proved out of his depth when leading armies. His background as the commander of Napoleon's headquarters Guard, the Guides of the Army of Italy, deprived him of the wide experience more deserving Marshals had earned before assuming high command. Like Murat, he was however an excellent cavalry commander and he also proved an able administrator of the Guard. His few attempts at independent command were not a success however and Napoleon thereafter preferred using Bessières as a leader of cavalry.

Bessières was not of high birth but he adopted the manners and looks of a gentleman as befitting Napoleon's closest Guard commander. He typically wore the uniform of Napoleon´s old Guides of the Army of Italy with Marshal´s distinctions and wore his hair long with white powder in Ancien Régime style, even when the latter went out of fashion. He was known to be well mannered and kind and generous to subordinates but very touchy about his privileges and position.